I have a question regarding parallelizing some of the bash scripts from the refinement and denovo prediction tutorials. They usually rely on GNU parallel to run across many cores, substituting some variable in the script with a number from the GNU parallel run command . I wonder how I can run the same scripts on a server running slurm workload manager, or any other possible multiprocessing strategy using Python.
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I am trying to clean this protein 3HZ7.pdb using pyrosetta.toolbox.cleaning.cleanATOM('3HZ7.pdb') in order to use it within PyRosetta.
The protein has MSE (Selenomethionine?) instead of MET at different parts of the sequence, therefore when applying cleanATOM() it just deletes these amino acids and I end up with a broken backbone (attached figure).
If I have a list of poses, how can I go about writing a single silent file that contains these poses? I see there's a SilentFilePoseInputStream class, but I can't find a way to output in silent format. Can someone point me to those functions?
Thanks in advance.
We are trying to install PyRosetta on CentOS 6. The current compilation of PyRosetta (PyRosetta4.Release.python27.linux.release-171.tar.bz2) requires GLIBC_2.14.
However, our system's GLIBC version is 2.12 and the compilation of PyRosetta stop with the error
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cm/shared/apps/pyrosetta/python/2.7/4.171/lib/python2.7/site-packages/pyrosetta-2018.9+release.333d996-py2.7-linux-x86_64.egg/pyrosetta/rosetta.so)
I have a database of dihedral angles in this order: residue psi psi. Is is possible to use pyrosetta to sample randomly throuh this database,
applying random psi and psi angles to a pdb pose, using a movemap? Imagine that my sequence is AQAAVFGT; so the script would retrieve randomly from the database the dihedrals corresponding to residues in the sequence and output a pose.
is this possible? Maybe with a loop with the SetTorsion mover?
So I'm trying to load this ligand_protein complex PDB into PyRosetta by temporarily creating a ResidueTypeSet
from pyrosetta import *
params_path = Vector1(['cefotaxime.params', 'cefotaxime.params'])
nonstandard_residue_type = generate_nonstandard_residue_set(params_path)
I got this error message:
generate_nonstandard_residue_set() takes exactly 2 arguments (1given)
I have seen references to minimization of a jump edge (e.g using a MinMover object) leading to both rotations and translations downstream of the jump.
I am modelling an interaction between two proteins, connected in the fold tree by a single jump edge, with atom pair constraints defined to bring them into close proximity.
I allow movement of this jump in the movemap (set_jump), atom_pair_constraints is activated in the scorefunction, and the fold tree is valid.
I'd like to create a function in rosetta (in C++) that ultimately will accept a python dictionary when called from pyrosetta. What's the best C++ class to use that will be the easiest for me to do the conversion from python dict? (i.e. is there any existing pyrosetta code that will convert a python dictionary to, say, a C++ map).
Thanks in advance.
I have a few questions regarding Pyrosetta 4:
First I have Anaconda2 which comes with python installed at /home/MYUSERNAME/anaconda2/bin/python, however the installation uses the default python at /usr/bin/python and its site packages directory in /usr/lib/python2.7/site-packages.
1) How can I uninstall pyrosetta?
2) How can I install it for the Anaconda python?
Second, running native python, trying >>> from rosetta import * gives:
I'm using pyrosetta compiled from rosetta_src_2017.39. I was wondering whether it's possible to use both talaris2014 and ref2015 in the same script. When I try to set up a scoring function using talaris2014 weights, I get this error:
pyrosetta.create_score_function("talaris2014") ERROR: talaris2014(.wts) requested, but -corrections::restore_talaris_behavior not set to true. This leads to a garbage scorefunction. Exiting.